One IGN article says the GC version is better.
[quote name='Andre Segers, IGN Guides']I vastly prefer the GCN version. Contrary to many reports, I didn't find the Wii aiming controls to be accurate at all - or rather, the lag induced by the cursor was enough to nullify any degree of accuracy it may have possessed. Oddly, Zelda is the only Wii game thus far that I have experienced any pointer problems with.
In addition, I found Navi's constant onscreen presence to detract from the experience, especially since she doesn't serve any function aside from showing the player where the cursor is when it's not in use - which isn't very useful (or necessary) at all. Granted, the pointer functionality can be turned off (and Navi by extension, thankfully), but then the main reason for purchasing the Wii version has thusly been removed.
As far as sword controls, I'll concede Wii's 'swinging' method was enjoyable, though ultimately unremarkable. After the novelty wears off, it neither enhances, nor detracts from the experience. But what has significantly changed is how the Spin Attack works. This vastly over-powered attack is a breeze to perform on the Wii version, and makes an already easy game appropriate for fetuses. The GCN version performs identically to previous 3D Zelda outings (i.e. Ocarina, Wind Waker) and is much more difficult to perform, thus preventing its abuse - a major enhancement in my opinion. The Wii version is akin to giving Master Chief a machine gun that launches rockets as the game's only weapon. Oh, and camera control is a good thing. I was skeptical of how much it would add to the GCN version, particularly since the game performs solidly on Wii, sans camera control, but after trying it out for myself, I must confess it's difficult to return to the Wii version. The flexibility of exploring the environment independent of the direction Link is running can't be overstated.[/quote]